is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1601913315/MOSAiCS-CTCF-GM12878-Rep1.relaxed.narrowPeak_1601913315 :  108749 peaks
 108749 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1601913315/MOSAiCS-CTCF-GM12878-Rep2.relaxed.narrowPeak_1601913315 :  123538 peaks
 123538  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-CTCF-GM12878-Rep1_VS_MOSAiCS-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-CTCF-GM12878-Rep1_VS_MOSAiCS-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1601913315/MOSAiCS-CTCF-GM12878-Rep1.relaxed.narrowPeak_1601913315
/nfs/nobackup/ensembl/akundaje/tmp/idr_1601913315/MOSAiCS-CTCF-GM12878-Rep2.relaxed.narrowPeak_1601913315
$p
[1] 0.8205716

$rho1
[1] 0.9037716

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-CTCF-GM12878-Rep1_VS_MOSAiCS-CTCF-GM12878-Rep2-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 36563.82

$x.mean2
[1] 59932.49

$y.mean1
[1] 35052.62

$y.mean2
[1] 66825.19

$x.sd1
[1] 21676.68

$x.sd2
[1] 22102.59

$y.sd1
[1] 21443.82

$y.sd2
[1] 12419.74